Applied Microbiology

Food and Drink Microbiology

Beer, Wine, and Spirits

Beer, wine, and spirits are made via fermentation, a process that converts the sugars in liquids to alcohol.

Since ancient times, people have been fermenting plant sugars to make alcohol. The most common alcoholic beverages are beer (made from grain, usually barley), wine (made from grapes), and distilled alcoholic beverages (spirits such as whiskey and gin).

Beer is made with hops, yeast, water, and grain, usually barley (occasionally, wheat, corn, rye, rice, or oats are substituted). The grain must be malted, or allowed to germinate, and the plant’s enzymes convert starches to sugar. The malted grains are then crushed, and hot water is added within a mixing tank to make mash, a mixture of sugary crushed grains and water. The mash is then transferred to a mash tun (a temperature-controlled container), where it is allowed to stand for several hours so that the water can draw the sugars out of the grains. Wort, a liquid containing high concentrations of the sugars that will be fermented, is then extracted from the mash. The wort is combined with hops for flavoring, and the mixture is boiled primarily to kill non-desirable fungi and bacterial spores, as well as to stop any further action by enzymes. Finally, a yeast in the genus Saccharomyces is added to begin the fermentation process. Saccharomyces is an excellent fermenter, or an organism that ferments sugars. Fermentation produces the ethanol (the alcoholic component of beer), and carbon dioxide (carbonation, or bubbles), and other substances that contribute to flavor and odor. The fermentation process lasts two to six weeks, after which the yeast is removed to stop further fermentation and the beer is filtered, pasteurized—partially sterilized through heat treatment or irradiation to make safe for consumption—and bottled.

The Brewing Process

For all beers the basic steps of the brewing process are the same, and yeast is a universal component, but the precise temperatures and durations of each step may vary. Additionally, sugars or flavors may be added to alter the taste.
Wine is made from juice, most commonly from grapes, although the juice of any fruit can be used. For wine made from grapes, the grapes are harvested and crushed and then pressed to make must, a fresh-pressed grape juice that contains the grape skin, seeds, and solids. For white wine the must is quickly filtered to separate the juice from the skins and solids, but for red wine the must is allowed to sit for a time so that the juice acquires the color and tannins from the skins, which impart additional flavor. Following separation of the juice from the solids, fermentation begins. This can be done naturally, using yeasts already present during harvesting. Many vintners, or people who make wine, use sulfur dioxide to kill any yeasts present and then introduce Saccharomyces yeast in precisely controlled quantities. Fermentation varies greatly for wine, lasting anywhere from 10 days to several months. Winemakers alter fermentation time to adjust and create unique wine flavors. In general, the longer a wine ferments, the more flavor characteristics it extracts from the grapes. At this point, the yeast is removed so that fermentation stops, and the wine is usually filtered, or clarified, and then stored for aging. Aging can last from mere weeks to decades, and it can take place in oak barrels or in the bottle in which the wine will be sold.

Spirits are made through distillation, the process of evaporating and condensing ethanol from an ethanol/water solution to produce a solution with a higher concentration of alcohol. The fermented products of many foods, including grains (whiskey, gin, and sake), potatoes (vodka), fruits (brandy), and molasses (rum), are distilled to give a large variety of spirits. The distillation process separates the volatile components, including ethanol and many components that add flavor, from nonvolatile components. Distillation increases the concentration of ethanol, usually in the range of 40% to 60%. Beer, in contrast, is typically 4% to 6% alcohol by volume, and wine is typically 11% to 14% alcohol by volume.


Cheese, a dairy product, is made via the action of microorganisms on solidified milk proteins.

Cheese is a dairy product typically made from the milk of cows, sheep, or goats. To begin, raw milk is treated with lactic acid bacteria, such as Lactobacillus and Lactococcus, which are bacteria that produce lactic acid and rennin. Rennin is an enzyme from the stomachs of calves used in making cheese by causing the milk to curdle. Genetically engineered bacteria can also produce recombinant forms of rennin. This prevents the need to sacrifice the calves. The bacteria sour the milk, and the enzymes coagulate the proteins in it into solids. A curd is solidified milk protein. Curds are separated from the whey, a liquid waste product of the cheese-making process. Different cheeses are treated differently at this point in the process—for soft cheeses the whey is drained from the curds by gravity, while for hard cheeses mechanical pressure is applied, sometimes along with heat, to ensure moisture is removed. Most cheeses are then salted, which both adds flavor and protects against spoilage. At this point, unripened cheeses, such as cream cheese, cottage cheese, and ricotta, are ready for packaging and consumption.

Most cheeses are ripened, which is the process by which microorganisms act on the cheese. Lactobacillus and Lactococcus are the two main genera of bacteria that ripen cheese. Bacteria from the Streptococcus genus are used for initial cheese ripening and also for yogurt making. Soft cheeses are usually ripened by microbes on the outside of the cheese, either those that occur naturally or ones that have been applied there. These microbes must diffuse inward, giving soft cheeses varying texture and flavor on the outside as compared to the inside of the cheese. For this reason, soft cheeses tend to be small. Hard cheeses, in contrast, are ripened by microbes occurring throughout the curd, so diffusion does not need to occur. This means that hard cheeses can be quite large. Hard cheeses also take longer to ripen than soft ones. Soft cheeses ripen for 1–5 months, whereas hard cheeses ripen for 2–16 months.

The Process of Cheese Making

Cheese making involves the mixing of rennin with milk to form curds and then separating the curds from the liquid component, or whey. It is then processed, pressed, and ripened for consumption. Bacteria aid in the fermentation process, and rennin can be obtained from recombinant bacteria.

Fermented Foods

Fermented foods, such as yogurt, pickles, and soy sauce, resist spoilage and have robust flavors and textures.

Fermented foods exist in nearly all cultures, as fermentation is an excellent method for prolonging the shelf life of foods. Common fermented foods include yogurt, vinegar, sauerkraut, and pickles. Several meats, such as summer sausage and salami, are also fermented.

Soy sauce is a fermented food product produced by a stepwise process. Crushed soybeans and wheat are treated with Aspergillus oryzae, a mold. This breaks down the starch in the plants to glucose, resulting in a product called koji. A salt solution is mixed with the koji to make a mixture called moromi, which is then fermented for 8–12 months. After fermentation, the liquid (now called soy sauce) is collected, while the solids are often used as animal feed. Miso is another fermented soy product, and is a paste made in a process similar to that in which soy sauce is made. Tofu is a soybean curd that has a texture similar to that of soft cheese. Cubes of tofu can be dipped in a solution of salt and citric acid and then inoculated with the fungus Mucor to make sufu, another fermented soy product. Tempeh is a fermented soy product that uses the whole soybean, unlike sufu, which uses only soybean curd. Tempeh is fermented by the fungus Rhizopus oryzae.

Other fermented foods include kimchi (a mixture of cabbage, radishes, carrots, and spices), kefir (a fermented milk product), kombucha (fermented tea), and fermented fish, such as anchovies and fish paste.
Aspergillus oryzae, a type of mold, is one of many microorganisms used to ferment foods. A. oryzae is used to make soy sauce by producing nutrients and fermenting the sugars in the food.
Credit: Forrest O.License: CC BY-SA 2.0

Contamination and Preservation

Microorganisms can spoil foods and make people sick, so methods such as pasteurization are used to kill microorganisms and preserve food and drink.

Microbes are used to make some foods and drinks, but they can also spoil them. In addition, pathogens can get on and into food and drinks. To combat this problem, many methods of preserving foods have been developed.

Pasteurization was discovered in 1856, when Louis Pasteur started investigating what caused beetroot alcohol to sour. Pasteurization is the process of heating liquids in the absence of oxygen to kill microbes that often make people sick or spoil liquids such as milk. Heated milk or other pasteurized liquids are then cooled and packaged for consumption. Two pasteurization procedures can be used, depending on the desired outcome for the liquid. High-temperature short-time (HTST) pasteurization exposes the liquid to a temperature of 72°C for 15 seconds. This is the pasteurization procedure used for the milk that most people buy at the grocery store. Liquids that undergo HTST must be refrigerated to prevent spoilage and will still spoil within a few weeks. Ultra-high temperature (UHT) pasteurization exposes the liquid to a temperature of 138°C for 2 or more seconds. This process more thoroughly kills microbes, allowing liquids to be stored for several months at room temperature. However, it also alters the structures of the proteins in the liquid, changing its flavor. UHT is commonly used for dairy products that are mixed with other liquids, such as coffee creamers.


Milk pasteurization takes place in an air-sealed vessel that is heated to a high enough temperature to denature microbial proteins that may be present, but not so high as to alter milk quality.
Milk is usually pasteurized, as are many varieties of juice. For many reasons, milk presents the greatest danger if consumed without pasteurization. First, the proteins and sugars in milk provide excellent nutrition to microbes. This means that microbes flourish in milk. Second, because milk comes from animals, pathogens such as Campylobacter jejuni, Salmonella typhi, Corynebacterium diphtheriae, and Streptococcus pyogenes on an animal's skin or infecting an animal's tissues can easily be transferred into the milk. Thus, it is vital that milk undergo pasteurization in order to make it safe to drink.

Other techniques used to preserve food include heating, cooling, desiccation, and irradiation. The temperature required to kill microbes in food varies from 60°C to 121°C, depending on the microbe and the type of food. The length of time varies as well, ranging from 20 minutes when temperatures are high to nearly two hours when temperatures are lower. Cooking food is an excellent method of killing microbes, because cooking temperatures typically exceed the 121°C required to kill microbes.

Cooling foods involves refrigeration at 4°C or freezing at –20°C. These methods rarely kill microbes; rather, they slow microbial growth, which allows the foods to be kept fresh longer. Desiccation, or dehydration, is the removal of water from a material—in other words, excessive drying. Desiccation is one of the oldest means of preserving food. Pemmican, beef jerky, and fruit leather are types of dessicated foods. Examples of foods that are freeze-dried, which is a combination of drying food and subjecting it to low temperatures, include coffee and fruits added to cereals. Irradiation, the act of using radiation to kill microorganisms, preserves food by dosing microbes on the food with ionizing radiation, which alters their genetic material, leading to death. Irradiation can be performed in the following ways: gamma ray, X-ray, or electron beam. Irradiated foods are not themselves radioactive, and they are safe to eat. The Food and Drug Administration has approved several foods for irradiation, including beef, pork, lettuce, spinach, shellfish, spices, and seasonings.